After I installed the OS and the Intel RST RAID utility, it shows the drive at a 6GB/s transfer rate. I looked in the BIOS and it still shows it at 3GB/s. I may have to run some tests to see if it is really running at 6GB/s even though the BIOS says otherwise (bug?).
As for the "Ext" in the (Ctrl+I) RAID utility, after loading the OS and Intel RST RAID utility, it does show one of the drives to be "external", even though it is most definitely internal. It doesn't seem to be the port either as the "Ext" follows the drive, no matter what port I plug it into. It also persists if I disable the eSATA function in the BIOS.